Re: [ccp4bb] Unmerged output from Scala

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Protein-detergent micelle sizes
From: Edward Berry eaberry {- at -} LBL {- dot -} GOV
Date: 2007-11-20

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Date: 2007-11-20

Subject: Re: Unmerged output from Scala
From: "Winter, G (Graeme)" g {- dot -} winter {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-11-20

Hi Hari,

You want the default options, pretty much - this discussion of rarely
used options is probably of more interest to methods developers. The
server is asking for F, SIGF so that is the merged structure factor
amplitudes from Truncate.

If you fire up ccp4i and use the scale / merge intensities task, ask to
run truncate (I think that this is the default anyway) and give it your
mosflm intensity file this should probably do the right things.

Cheers,

Graeme

________________________________

From: hari jayaram [mailto:harijay@gmail.com]
Sent: 19 November 2007 22:52
To: Clemens Vonrhein; Winter, G (Graeme); CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Unmerged output from Scala

Hello all,
Along the lines of SCALA options UNMERGED and NOSCALE.. I am a little
confused..

I wanted to get my data from mosflm to be used for the anisotropic
scaling and ellipsoidal truncation server at
http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/

I was wondering what SCALA/Truncate options I need to use to obtain my
F and SIG F for the analysis
Thanks
Hari Jayaram
Postdoc, Brandeis University

On Nov 19, 2007 3:53 PM, Clemens Vonrhein
wrote:

Hi Graeme,

even with these options (ONLYMERGE and SCALES CONSTANT) you will
have
the SCALE column applied again to the intensities (not good) -
at
least that's how I understood Phil. You need to use

ONLYMERGE
INSCALE OFF

to use the already scaled intensities and avoid applying the
SCALE
column again - Phil was the one telling me that. I was
scratching my
head for a long time trying to understand those various
INTIAL/ONLYMERGE/INSCALE/NOSCALE options and how they relate to
each
other ...

Cheers

Clemens

On Mon, Nov 19, 2007 at 08:07:02PM -0000, Winter, G (Graeme)
wrote:
> Hi Phil,
>
> I use this option but not these columns. The only time I feed
the file back I use "ONLYMERGE" and "SCALES CONSTANT", to remerge the
reflections.
>
> Cheers,
>
> Graeme
>
> ________________________________
>
> From: CCP4 bulletin board on behalf of Phil Evans
> Sent: Mon 19/11/2007 5:07 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Unmerged output from Scala
>
>
>
> Is anyone using the OUTPUT UNMERGED option in Scala?
>
> This file contains columns called SCALE & SIGSCALE which are
the
> applied scale and its SD
>
> I propose to change the names of these columns so that if you
put
> the file back into Scala the scales do not get re-applied by
default
> (which is wrong since they have been applied already)
>
> Will this cause anyone problems? I suspect that very few
people or
> programs are using this file
>
> Phil Evans
>

--

***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Protein-detergent micelle sizes
From: Edward Berry eaberry {- at -} LBL {- dot -} GOV
Date: 2007-11-20

Next message:
Subject: Very low B factor
From: Jobichen Chacko jobichenc {- at -} NUS {- dot -} EDU {- dot -} SG
Date: 2007-11-20